piggyback - Managing Larger Data on a GitHub Repository

Helps store files as GitHub release assets, which is a convenient way for large/binary data files to piggyback onto public and private GitHub repositories. Includes functions for file downloads, uploads, and managing releases via the GitHub API.

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data-storegit-lfspeer-reviewed

12.21 score 201 stars 16 dependents 286 scripts 25k downloads

EML - Read and Write Ecological Metadata Language Files

Work with Ecological Metadata Language ('EML') files. 'EML' is a widely used metadata standard in the ecological and environmental sciences, described in Jones et al. (2006), <doi:10.1146/annurev.ecolsys.37.091305.110031>.

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emleml-metadatametadata-standard

11.38 score 99 stars 10 dependents 416 scripts 1.0k downloads

knitcitations - Citations for 'Knitr' Markdown Files

Provides the ability to create dynamic citations in which the bibliographic information is pulled from the web rather than having to be entered into a local database such as 'bibtex' ahead of time. The package is primarily aimed at authoring in the R 'markdown' format, and can provide outputs for web-based authoring such as linked text for inline citations. Cite using a 'DOI', URL, or 'bibtex' file key. See the package URL for details.

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10.95 score 219 stars 4 dependents 886 scripts 4.8k downloads

rfishbase - R Interface to 'FishBase'

A programmatic interface to 'FishBase', re-written based on an accompanying 'RESTful' API. Access tables describing over 30,000 species of fish, their biology, ecology, morphology, and more. This package also supports experimental access to 'SeaLifeBase' data, which contains nearly 200,000 species records for all types of aquatic life not covered by 'FishBase.'

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fishfishbasetaxonomy

10.27 score 123 stars 3 dependents 808 scripts 2.0k downloads

rdflib - Tools to Manipulate and Query Semantic Data

The Resource Description Framework, or 'RDF' is a widely used data representation model that forms the cornerstone of the Semantic Web. 'RDF' represents data as a graph rather than the familiar data table or rectangle of relational databases. The 'rdflib' package provides a friendly and concise user interface for performing common tasks on 'RDF' data, such as reading, writing and converting between the various serializations of 'RDF' data, including 'rdfxml', 'turtle', 'nquads', 'ntriples', and 'json-ld'; creating new 'RDF' graphs, and performing graph queries using 'SPARQL'. This package wraps the low level 'redland' R package which provides direct bindings to the 'redland' C library. Additionally, the package supports the newer and more developer friendly 'JSON-LD' format through the 'jsonld' package. The package interface takes inspiration from the Python 'rdflib' library.

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peer-reviewed

10.25 score 61 stars 7 dependents 190 scripts 3.5k downloads

RNeXML - Semantically Rich I/O for the 'NeXML' Format

Provides access to phyloinformatic data in 'NeXML' format. The package should add new functionality to R such as the possibility to manipulate 'NeXML' objects in more various and refined way and compatibility with 'ape' objects.

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metadatanexmlphylogeneticslinked-data

10.22 score 15 stars 20 dependents 94 scripts 7.1k downloads

codemetar - Generate 'CodeMeta' Metadata for R Packages

The 'Codemeta' Project defines a 'JSON-LD' format for describing software metadata, as detailed at <https://codemeta.github.io>. This package provides utilities to generate, parse, and modify 'codemeta.json' files automatically for R packages, as well as tools and examples for working with 'codemeta.json' 'JSON-LD' more generally.

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metadatacodemetaropenscicitationcreditlinked-datajson-ldpeer-reviewed

9.05 score 67 stars 6 dependents 49 scripts 755 downloads

duckdbfs - High Performance Remote File System, Database and 'Geospatial' Access Using 'duckdb'

Provides friendly wrappers for creating 'duckdb'-backed connections to tabular datasets ('csv', parquet, etc) on local or remote file systems. This mimics the behaviour of "open_dataset" in the 'arrow' package, but in addition to 'S3' file system also generalizes to any list of 'http' URLs.

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8.75 score 101 stars 6 dependents 186 scripts 1.7k downloads

emld - Ecological Metadata as Linked Data

This is a utility for transforming Ecological Metadata Language ('EML') files into 'JSON-LD' and back into 'EML.' Doing so creates a list-based representation of 'EML' in R, so that 'EML' data can easily be manipulated using standard 'R' tools. This makes this package an effective backend for other 'R'-based tools working with 'EML.' By abstracting away the complexity of 'XML' Schema, developers can build around native 'R' list objects and not have to worry about satisfying many of the additional constraints of set by the schema (such as element ordering, which is handled automatically). Additionally, the 'JSON-LD' representation enables the use of developer-friendly 'JSON' parsing and serialization that may facilitate the use of 'EML' in contexts outside of 'R,' as well as the informatics-friendly serializations such as 'RDF' and 'SPARQL' queries.

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8.15 score 14 stars 11 dependents 77 scripts 1.0k downloads

contentid - An Interface for Content-Based Identifiers

An interface for creating, registering, and resolving content-based identifiers for data management. Content-based identifiers rely on the 'cryptographic' hashes to refer to the files they identify, thus, anyone possessing the file can compute the identifier using a well-known standard algorithm, such as 'SHA256'. By registering a URL at which the content is accessible to a public archive (such as Hash Archive) or depositing data in a scientific repository such 'Zenodo', 'DataONE' or 'SoftwareHeritage', the content identifier can serve many functions typically associated with A Digital Object Identifier ('DOI'). Unlike location-based identifiers like 'DOIs', content-based identifiers permit the same content to be registered in many locations.

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8.03 score 46 stars 3 dependents 131 scripts 4.0k downloads

taxadb - A High-Performance Local Taxonomic Database Interface

Creates a local database of many commonly used taxonomic authorities and provides functions that can quickly query this data.

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7.78 score 44 stars 1 dependents 74 scripts 1.0k downloads

earthdatalogin - NASA 'EarthData' Access Utilities

Providing easy, portable access to NASA 'EarthData' products through the use of bearer tokens. Much of NASA's public data catalogs hosted and maintained by its 12 Distributed Active Archive Centers ('DAACs') are now made available on the Amazon Web Services 'S3' storage. However, accessing this data through the standard 'S3' API is restricted to only to compute resources running inside 'us-west-2' Data Center in Portland, Oregon, which allows NASA to avoid being charged data egress rates. This package provides public access to the data from any networked device by using the 'EarthData' login application programming interface (API), <https://www.earthdata.nasa.gov/data/earthdata-login>, providing convenient authentication and access to cloud-hosted NASA 'EarthData' products. This makes access to a wide range of earth observation data from any location straight forward and compatible with R packages that are widely used with cloud native earth observation data (such as 'terra', 'sf', etc.)

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7.58 score 28 stars 90 scripts 508 downloads

arkdb - Archive and Unarchive Databases Using Flat Files

Flat text files provide a robust, compressible, and portable way to store tables from databases. This package provides convenient functions for exporting tables from relational database connections into compressed text files and streaming those text files back into a database without requiring the whole table to fit in working memory.

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archivingdatabasedbipeer-reviewed

7.29 score 80 stars 41 scripts 486 downloads

treebase - Discovery, Access and Manipulation of 'TreeBASE' Phylogenies

Interface to the API for 'TreeBASE' <http://treebase.org> from 'R.' 'TreeBASE' is a repository of user-submitted phylogenetic trees (of species, population, or genes) and the data used to create them.

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6.65 score 10 stars 1 dependents 50 scripts 240 downloads

codemeta - A Smaller 'codemetar' Package

The 'Codemeta' Project defines a 'JSON-LD' format for describing software metadata, as detailed at <https://codemeta.github.io>. This package provides core utilities to generate this metadata with a minimum of dependencies.

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metadatacodemetaropenscicitationcreditlinked-data

6.21 score 8 stars 7 dependents 15 scripts 783 downloads

gbifdb - High Performance Interface to 'GBIF'

A high performance interface to the Global Biodiversity Information Facility, 'GBIF'. In contrast to 'rgbif', which can access small subsets of 'GBIF' data through web-based queries to a central server, 'gbifdb' provides enhanced performance for R users performing large-scale analyses on servers and cloud computing providers, providing full support for arbitrary 'SQL' or 'dplyr' operations on the complete 'GBIF' data tables (now over 1 billion records, and over a terabyte in size). 'gbifdb' accesses a copy of the 'GBIF' data in 'parquet' format, which is already readily available in commercial computing clouds such as the Amazon Open Data portal and the Microsoft Planetary Computer, or can be accessed directly without downloading, or downloaded to any server with suitable bandwidth and storage space. The high-performance techniques for local and remote access are described in <https://duckdb.org/why_duckdb> and <https://arrow.apache.org/docs/r/articles/fs.html> respectively.

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6.15 score 40 stars 35 scripts 187 downloads

virtuoso - Interface to 'Virtuoso' using 'ODBC'

Provides users with a simple and convenient mechanism to manage and query a 'Virtuoso' database using the 'DBI' (Data-Base Interface) compatible 'ODBC' (Open Database Connectivity) interface. 'Virtuoso' is a high-performance "universal server," which can act as both a relational database, supporting standard Structured Query Language ('SQL') queries, while also supporting data following the Resource Description Framework ('RDF') model for Linked Data. 'RDF' data can be queried using 'SPARQL' ('SPARQL' Protocol and 'RDF' Query Language) queries, a graph-based query that supports semantic reasoning. This allows users to leverage the performance of local or remote 'Virtuoso' servers using popular 'R' packages such as 'DBI' and 'dplyr', while also providing a high-performance solution for working with large 'RDF' 'triplestores' from 'R.' The package also provides helper routines to install, launch, and manage a 'Virtuoso' server locally on 'Mac', 'Windows' and 'Linux' platforms using the standard interactive installers from the 'R' command-line. By automatically handling these setup steps, the package can make using 'Virtuoso' considerably faster and easier for a most users to deploy in a local environment. Managing the bulk import of triples from common serializations with a single intuitive command is another key feature of this package. Bulk import performance can be tens to hundreds of times faster than the comparable imports using existing 'R' tools, including 'rdflib' and 'redland' packages.

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6.06 score 10 stars 19 scripts 205 downloads

minioclient - Interface to the 'MinIO' Client

An R interface to the 'MinIO' Client. The 'MinIO' Client ('mc') provides a modern alternative to UNIX commands like 'ls', 'cat', 'cp', 'mirror', 'diff', 'find' etc. It supports 'filesystems' and Amazon "S3" compatible cloud storage service ("AWS" Signature v2 and v4). This package provides convenience functions for installing the 'MinIO' client and running any operations, as described in the official documentation, <https://min.io/docs/minio/linux/reference/minio-mc.html?ref=docs-redirect>. This package provides a flexible and high-performance alternative to 'aws.s3'.

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5.29 score 25 stars 78 scripts 242 downloads

roxigraph - 'RDF' and 'SPARQL' for R using 'Oxigraph'

Provides 'RDF' storage and 'SPARQL' 1.1 query capabilities by wrapping the 'Oxigraph' graph database library <https://github.com/oxigraph/oxigraph>. Supports in-memory and persistent ('RocksDB') storage, multiple 'RDF' serialization formats ('Turtle', 'N-Triples', 'RDF-XML', 'N-Quads', 'TriG'), and full 'SPARQL' 1.1 Query and Update support. Built using the 'extendr' framework for 'Rust'-R bindings.

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rustcargo

4.95 score 3 stars 5 scripts 255 downloads

neonstore - NEON Data Store

The National Ecological Observatory Network (NEON) provides access to its numerous data products through its REST API, <https://data.neonscience.org/data-api/>. This package provides a high-level user interface for downloading and storing NEON data products. Unlike 'neonUtilities', this package will avoid repeated downloading, provides persistent storage, and improves performance. 'neonstore' can also construct a local 'duckdb' database of stacked tables, making it possible to work with tables that are far to big to fit into memory.

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databaseecologyneon-dataprovenance

4.83 score 9 stars 149 scripts 495 downloads

pmc - Phylogenetic Monte Carlo

Monte Carlo based model choice for applied phylogenetics of continuous traits. Method described in Carl Boettiger, Graham Coop, Peter Ralph (2012) Is your phylogeny informative? Measuring the power of comparative methods, Evolution 66 (7) 2240-51. <doi:10.1111/j.1558-5646.2011.01574.x>.

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4.64 score 2 stars 11 scripts 277 downloads

sarsop - Approximate POMDP Planning Software

A toolkit for Partially Observed Markov Decision Processes (POMDP). Provides bindings to C++ libraries implementing the algorithm SARSOP (Successive Approximations of the Reachable Space under Optimal Policies) and described in Kurniawati et al (2008), <doi:10.15607/RSS.2008.IV.009>. This package also provides a high-level interface for generating, solving and simulating POMDP problems and their solutions.

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decision-theoryfisheriespomdp

4.58 score 11 stars 23 scripts 222 downloads

EcoNetGen - Simulate and Sample from Ecological Interaction Networks

Randomly generate a wide range of interaction networks with specified size, average degree, modularity, and topological structure. Sample nodes and links from within simulated networks randomly, by degree, by module, or by abundance. Simulations and sampling routines are implemented in 'FORTRAN', providing efficient generation times even for large networks. Basic visualization methods also included. Algorithms implemented here are described in de Aguiar et al. (2017) <arXiv:1708.01242>.

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fortran

4.04 score 10 stars 11 scripts 241 downloads

rcloner - Interface to 'rclone' Cloud Storage Utility

Provides an R interface to 'rclone' <https://rclone.org>, a command-line program for managing files on cloud storage. 'rclone' supports over 40 cloud storage providers including 'S3'-compatible services ('Amazon S3', 'MinIO', 'Ceph'), 'Google Cloud Storage', 'Azure Blob Storage', and many others. This package downloads and manages the 'rclone' binary automatically and wraps its commands as R functions, returning results as data frames where appropriate.

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4.00 score 2 stars 3 scripts 447 downloads

taxalight - A Lightweight and Lightning-Fast Taxonomic Naming Interface

Creates a local Lightning Memory-Mapped Database ('LMDB') of many commonly used taxonomic authorities and provides functions that can quickly query this data. Supported taxonomic authorities include the Integrated Taxonomic Information System ('ITIS'), National Center for Biotechnology Information ('NCBI'), Global Biodiversity Information Facility ('GBIF'), Catalogue of Life ('COL'), and Open Tree Taxonomy ('OTT'). Name and identifier resolution using 'LMDB' can be hundreds of times faster than either relational databases or internet-based queries. Precise data provenance information for data derived from naming providers is also included.

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taxonomy

3.89 score 5 stars 4 scripts 3.1k downloads

rgpdd - R Interface to the Global Population Dynamics Database

R Interface to the Global Population Dynamics Database (<https://ecologicaldata.org/wiki/global-population-dynamics-database>)

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3.78 score 8 stars 15 scripts